Paint with FillBrush
The Fill Brush does not do what you are expecting it to do.

The fill brush simply fills the entire image, irregardless of color, back facing, occluded faces or anything else. That is true when used in the UV Image Editor or the 3D view.

There is no way with the fill brush to fill just one color, like can be done with in photoshop's paint bucket tool.

The only way you can limit the fill brush's reach is by masking the faces.


In texture paint mode hit Tab, that will bring you to edit mode. 
Select the faces you want to paint.
Press Tab again to go back to texture paint mode. Now press M to turn on the masking feature. (Do note that you can select and unselect faces in texture pain mode when the masking is turned on by  ShiftRMB  on the faces.)
Now when you use the Fill Brush it will only effect the selected faces.